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Born in Palmyra, New York, his family moved to Pennsylvania, back to New York, to Ohio then to Louisville, Kentucky (1827–1830) then back to Ohio while his father, Seneca Lapham, worked on the canals in various locations. Lapham was of entirely English ancestry, all of which had been in what is now the United States since the early 1600s. His ancestors were among the first English colonists to establish Rhode Island.[3] He displayed a talent for scientific observation early on while working on the canals and their locks himself, producing drawings that he could sell at the age of thirteen.

In July 1836, Lapham moved to Kilbourntown (which soon incorporated into the city of Milwaukee, Wisconsin) and worked closely with Byron Kilbourn in his business and development endeavors.[4] The two had worked together previously on the Miami Canal and Lapham considered him a loyal friend and mentor. Before the end of the year, Lapham had published a Catalogue of Plants and Shells, Found in the vicinity of Milwaukee, on the West Side of Lake Michigan, perhaps the first scientific work published west of the Great Lakes.

In 1848,[5] Lapham founded the Wisconsin Natural History Association, a predecessor of the Wisconsin Academy of Sciences, Arts, and Letters,[6] of which he also was a charter member.

Many of his works and early maps were used for various civil projects such as canal and railroad development. In 1844 Lapham published the first substantial book on the geography of the Wisconsin Territory. His first map of Wisconsin was made in 1846.[7] He published many more papers and books through his life, particularly on geology, archaeology and history, and flora and fauna of Wisconsin, including publication by the Smithsonian Institution.[8]

Lapham is considered "Wisconsin's first great scientist"[12] and the "Father of the U.S Weather Service,"[13][14] based upon his lobbying to Congress and the Smithsonian Institution to create such an agency to forecast storms on the Great Lakes and both coasts.[15] When the agency was created through the U.S. Secretary of War, Lapham made the first such accurate Great Lakes storm warning from Chicago.[16]